diff --git a/data/label_raw/230804_strain_peptides_antibiogram_Enterobacterales.xlsx b/data/label_raw/230804_strain_peptides_antibiogram_Enterobacterales.xlsx index ed86b8afffd856bdcba65bda4fd2ecdcbca22f4b..9eac0e6767acd1bec18f6b978fc51e498dd54f7d 100644 Binary files a/data/label_raw/230804_strain_peptides_antibiogram_Enterobacterales.xlsx and b/data/label_raw/230804_strain_peptides_antibiogram_Enterobacterales.xlsx differ diff --git a/image_ref/grad_cam.py b/image_ref/grad_cam.py index 139bcd234d064d44ec834977b553b751176588c1..b70b5f2736544feeb1b8a1f9da1fda1c2890e151 100644 --- a/image_ref/grad_cam.py +++ b/image_ref/grad_cam.py @@ -2,15 +2,12 @@ import numpy as np import torch import cv2 from torchvision.transforms import transforms - -from image_ref.config import load_args_contrastive from image_ref.dataset_ref import Threshold_noise, Log_normalisation, npy_loader from image_ref.main import load_model from image_ref.model import Classification_model_duo_contrastive -def compute_class_activation_map(): - args = load_args_contrastive() +def compute_class_activation_map(path_aer, path_ana, path_ref, model_path, model_type='Resnet18'): transform = transforms.Compose( [transforms.Resize((224, 224)), @@ -22,13 +19,8 @@ def compute_class_activation_map(): [transforms.Resize((224, 224)), transforms.Normalize(0.5, 0.5)]) - model_path = '../saved_model/baseline_resnet18_contrastive_prop_30_bis.pt' - path_aer ='../data/processed_data/npy_image/data_test_contrastive/Citrobacter freundii/CITFRE17_AER.npy' - path_ana ='../data/processed_data/npy_image/data_test_contrastive/Citrobacter freundii/CITFRE17_ANA.npy' - # path_ref ='../image_ref/img_ref/Citrobacter freundii.npy' #positive - # path_ref = '../image_ref/img_ref/Enterobacter hormaechei.npy' #negative - path_ref = '../image_ref/img_ref/Proteus mirabilis.npy' # negative + tensor_aer = npy_loader(path_aer) tensor_ana = npy_loader(path_ana) tensor_ref = npy_loader(path_ref) @@ -44,12 +36,11 @@ def compute_class_activation_map(): tensor_ref = torch.unsqueeze(tensor_ref, dim=0) - model = Classification_model_duo_contrastive(model=args.model, n_class=2) + model = Classification_model_duo_contrastive(model=model_type, n_class=2) model.double() # load weight - if args.pretrain_path is not None: - load_model(model, model_path) - print('model loaded') + load_model(model, model_path) + print('model loaded') # Identify the target layer target_layer = model.im_encoder.layer4[-1] @@ -112,24 +103,11 @@ def compute_class_activation_map(): return heatmap if __name__ =='__main__': - # compute_class_activation_map() - - transform = transforms.Compose( - [transforms.Resize((224, 224)), - Threshold_noise(500), - Log_normalisation(), - transforms.Normalize(0.5, 0.5)]) - - ref_transform = transforms.Compose( - [transforms.Resize((224, 224)), - Threshold_noise(0), - Log_normalisation(), - transforms.Normalize(0.5, 0.5) - ]) - - path_ref = '../image_ref/img_ref/Enterobacter hormaechei.npy' # negative - tensor_ref = npy_loader(path_ref) + model_path = '../saved_model/baseline_resnet18_contrastive_prop_30_bis.pt' + path_aer ='../data/processed_data/npy_image/data_test_contrastive/Citrobacter freundii/CITFRE17_AER.npy' + path_ana ='../data/processed_data/npy_image/data_test_contrastive/Citrobacter freundii/CITFRE17_ANA.npy' + # path_ref ='../image_ref/img_ref/Citrobacter freundii.npy' #positive + # path_ref = '../image_ref/img_ref/Enterobacter hormaechei.npy' #negative + path_ref = '../image_ref/img_ref/Proteus mirabilis.npy' # negative - ref_base = tensor_ref.squeeze() - ref_false = transform(tensor_ref).squeeze() - ref_true = ref_transform(tensor_ref).squeeze() \ No newline at end of file + compute_class_activation_map(path_aer, path_ana, path_ref, model_path)